Mapping the nanoscale organisation of cellular proteins across complex topographies

PGR-P-1114

Key facts

Type of research degree: PhD
Application deadline: Ongoing deadline
Project start date: Wednesday 1 October 2025
Country eligibility: International (open to all nationalities, including the UK)
Funding: Non-funded
Supervisors: Dr Aleks Ponjavic and Dr Ralf Richter
Schools: School of Physics and Astronomy
Research groups/institutes: Molecular and Nanoscale Physics

<h2 class="heading hide-accessible">Summary</h2>

Super-resolution fluorescence microscopy techniques make it possible to visualise nanoscale structures in cells, by going beyond the capabilities of conventional microscopy. Over the past decade, this has led to a series of new biological discoveries such as revealing the molecular organisation of the genome and how proteins interact to fulfil vital cellular processes. However, there are major challenges when it comes to imaging nanoscale structures within the cell membrane due to its complex topography. There is a need for techniques that can image nanoscopic structures over large spatial scales as well as novel analysis tools that can unravel the interplay between subcellular organisation and biological processes. In this project, you will apply point-spread-function engineering [1] and light-sheet microscopy [2] to optimise and develop novel large depth-of-field super-resolution microscopy methodologies. This will be used for nanoscopic mapping of protein organisation in entire cells that is vital e.g. for understanding the basic mechanisms involved in the immune response [3] and the influence of DNA folding on genomic processing [4]. This interdisciplinary work spans multiple research areas including: optical engineering, computational analysis (including deep learning approaches), fluorescent probe optimisation and biophysics (applying super-resolution microscopy to understand cellular processes, particularly within immunology). This offers flexibility in terms of tailoring the research direction to your interests. This project will take place in the Molecular and Nanoscale Physics Group within the School of Physics and Astronomy, under joint supervision with Dr Ralf Richter and with external collaborators in the Schools of Engineering, Biology and Medicine. Candidates should have a background in physics, engineering, chemistry or a closely related field and a keen interest in method development. References: 1 Carr, A.R., Ponjavic, A. et al. 2017. Three-dimensional super-resolution in eukaryotic cells using the double-helix point spread function. Biophysical journal, 112(7), pp.1444-1454. 2 Ponjavic, A., McColl, J. et al. 2018. Single-molecule light-sheet imaging of suspended T cells. Biophysical journal, 114(9), pp.2200-2211. 3 Santos, A. M., Ponjavic, A. et al. 2018. Capturing resting T cells: the perils of PLL. Nature immunology, 19(3), 203-205. 4 Di Antonio, M., Ponjavic, A. et al. 2020. Single-molecule visualization of DNA G-quadruplex formation in live cells. Nature chemistry, 12(9), 832-837.

<h2 class="heading">How to apply</h2>

Formal applications for research degree study should be made online through the <a href="http://www.leeds.ac.uk/rsa/prospective_students/apply/I_want_to_apply.html">University's website</a>. Please state clearly in Planned Course of Study that you are applying for PHD Physics & Astronomy FT, in the research information section that the research degree you wish to be considered for is Mapping the nanoscale organisation of cellular proteins across complex topographies as well as <a href="https://eps.leeds.ac.uk/physics/staff/8090/dr-aleks-ponjavic">Dr Aleks Ponjavic</a> as your proposed supervisor and in the finance section, please state clearly the funding that you are applying for, if you are self-funding or externally sponsored. If English is not your first language, you must provide evidence that you meet the University's minimum English language requirements (below). As an international research-intensive university, we welcome students from all walks of life and from across the world. We foster an inclusive environment where all can flourish and prosper, and we are proud of our strong commitment to student education. Across all Faculties we are dedicated to diversifying our community and we welcome the unique contributions that individuals can bring, and particularly encourage applications from, but not limited to Black, Asian, people who belong to a minority ethnic community, people who identify as LGBT+ and people with disabilities. Applicants will always be selected based on merit and ability. Applications will be considered on an ongoing basis. Potential applicants are strongly encouraged to contact the supervisors for an informal discussion before making a formal application. We also advise that you apply at the earliest opportunity as the application and selection process may close early, should we receive a sufficient number of applications or that a suitable candidate is appointed. Please note that you must provide the following documents in support of your application by the closing date of Monday 3 March 2025 if applying for Leeds Doctoral Scholarship or Tuesday 1 April 2025 for Leeds Opportunity Research Scholarship. If you are applying with external sponsorship or you are funding your own study, please ensure you provide your supporting documents at the point you submit your application: <ul> <li>Full Transcripts of all degree study or if in final year of study, full transcripts to date</li> <li>Personal Statement outlining your interest in the project</li> <li>CV</li> </ul>

<h2 class="heading heading--sm">Entry requirements</h2>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree. Applicants are advised to check with the relevant School prior to making an application. Applicants who are uncertain about the requirements for a particular research degree are advised to contact the School or Graduate School prior to making an application.

<h2 class="heading heading--sm">English language requirements</h2>

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid. Some schools and faculties have a higher requirement.

<h2 class="heading">Funding on offer</h2>

Self-Funded or externally sponsored students are welcome to apply. UK – The <a href="https://phd.leeds.ac.uk/funding/138-leeds-doctoral-scholarship-2025-faculty-of-engineering-and-physical-sciences#:~:text=Key%20facts&text=One%20Leeds%20Doctoral%20Scholarship%20is,rata%20for%20part%2Dtime%20study.">Leeds Doctoral Scholarship</a> (closing date: Monday 3 March 2025) and <a href="https://phd.leeds.ac.uk/funding/234-leeds-opportunity-research-scholarship-2022">Leeds Opportunity Research Scholarship</a> (closing date: Tuesday 1 April 2025) are available to UK applicants. The <a href="https://phd.leeds.ac.uk/funding/102-bell-burnell-scholarship-award-awarded-by-the-iop">Bell Burnell Scholarship Award</a> is available to support applicants who are from groups that are currently under-represented in physics (awarded by the IOP) (now closed for October 2025 entry). <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds. Non-UK – The <a href="https://phd.leeds.ac.uk/funding/48-china-scholarship-council-university-of-leeds-scholarships-2021">China Scholarship Council - University of Leeds Scholarship</a> is available to nationals of China (now closed for October 2025 entry). The <a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a> is available to support US citizens. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds. You will be responsible for paying the overtime fee in full in your writing up/overtime year (£320 in Session 2024/25), but the scholarship maintenance allowance will continue to be paid for up to 6 months in the final year of award. Important: Please note that that the award does not cover the costs associated with moving to the UK. All such costs (<a href="https://www.leeds.ac.uk/international-visas-immigration/doc/applying-student-visa">visa, Immigration Health Surcharge</a>, flights etc) would have to be met by yourself, or you will need to find an alternative funding source. Please refer to the <a href="https://www.ukcisa.org.uk/">UKCISA</a> website for information regarding Fee Status for Non-UK Nationals.

<h2 class="heading">Contact details</h2>

Individuals interested in this project are encouraged to contact Dr. Aleks Ponjavic by email to <a href="mailto:a.ponjavic@leeds.ac.uk">a.ponjavic@leeds.ac.uk</a> for further information. For questions related to the application process and eligibility, please contact PGR Admissions by email to <a href="mailto:maps.pgr.admissions@leeds.ac.uk">maps.pgr.admissions</a><a href="mailto:EMAIL@leeds.ac.uk">@leeds.ac.uk</a>